Methods of colonizing a microbiome, treating and/or preventing inflammatory bowel disease and graft versus host disease

Abstract

The disclosure relates to methods for colonizing a microbiome, by administering pharmaceutical compositions comprising a purified bacterial mixture to the subject. Also provided are methods for treating and/or preventing inflammatory bowel disease, methods for reducing the risk of inflammatory bowel disease and/or reducing the occurrence of inflammatory bowel disease in a subject by administering pharmaceutical compositions comprising a purified bacterial mixture to the subject. Also provided are methods for treating and/or preventing graft versus host disease in a subject by administering pharmaceutical compositions comprising a purified bacterial mixture to the subject.

1 . A method for colonizing a microbiome in a subject, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising a purified bacterial mixture comprising two or more bacterial strains of species selected from the group consisting of  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         2 . The method of  claim 1 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen, bacterial strains. 
     
     
         3 . The method of  claim 1 or 2 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         4 . The method of  claim 3 , wherein the subject has, is suspected of having, or is at risk of having inflammatory bowel disorder (IBD). 
     
     
         5 . The method of  claim 1 or 2 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium hathewayi, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Eubacterium contortum, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         6 . The method of  claim 5 , wherein the subject has, is suspected of having, or is at risk of having graft versus host disease (GvHD). 
     
     
         7 . A method for colonizing a microbiome in a subject, the method comprising administering to the subject a therapeutically effective of a pharmaceutical composition comprising a purified bacterial mixture comprising two or more bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         8 . The method of  claim 7 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen bacterial strains. 
     
     
         9 . The method of  claim 7 or 8 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs:1-16. 
     
     
         10 . The method of  claim 9 , wherein the subject has, is suspected of having, or is at risk of having inflammatory bowel disorder (IBD). 
     
     
         11 . The method of  claim 10 , wherein the IBD is ulcerative colitis or Crohn's disease. 
     
     
         12 . The method of  claim 10 or 11 , wherein the subject has one or more risk factors associated with IBD. 
     
     
         13 . The method of  claim 7 or 8 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs:3, 5-10, 12, and 14-16. 
     
     
         14 . The method of  claim 13 , wherein the subject has, is suspected of having, or is at risk of having graft versus host disease (GvHD). 
     
     
         15 . The method of any one of  claims 1-14 , wherein each of the bacterial strains of the pharmaceutical composition colonizes the microbiome. 
     
     
         16 . The method of any one of  claims 1-15 , wherein the bacterial strains of the pharmaceutical composition colonize the microbiome over an extended period of time. 
     
     
         17 . The method of any one of  claims 1-16 , wherein the pharmaceutical composition reduces an amount of one or more primary bile acids in the subject. 
     
     
         18 . The method of  claim 17 , wherein the primary bile acid is chenodeoxycholic acid, cholic acid, glycochenodeoxycholic acid, glycocholic acid, taurochenodeoxycholic acid, or taurocholic acid. 
     
     
         19 . The method of any one of  claims 1-18 , wherein the pharmaceutical composition reduces levels of primary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         20 . The method of any one of  claims 1-19 , wherein the pharmaceutical composition increases an amount of one or more secondary bile acids in the subject. 
     
     
         21 . The method of  claim 20 , wherein the secondary bile acid is alloiso isolithocholic acid, dehydrolithocholic acid, deoxycholic acid, glycodeoxycholic acid, glycoursodeoxycholic acid, lithocholic acid, taurodeoxcycholic acid, or ursodeoxycholic acid. 
     
     
         22 . The method of any one of  claims 1-21 , wherein the pharmaceutical composition increases levels of secondary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         23 . The method of any one of  claims 1-22 , wherein the pharmaceutical composition increases an amount of one or more short-chain fatty acids (SCFAs) in the subject. 
     
     
         24 . The method of  claim 23 , wherein the SCFA is 2-methylbutyric acid, acetic acid, butyric acid, hexanoic acid, isobutyric acid, isovaleric acid, propionic acid, or valeric acid. 
     
     
         25 . The method of any one of  claims 1-24 , wherein the pharmaceutical composition increases levels of short-chain fatty acids (SCFAs) in the subject by 2-fold to 100,000-fold. 
     
     
         26 . The method of any one of  claims 1-25 , wherein the pharmaceutical composition increases an amount of one or more indoles in the subject. 
     
     
         27 . The method of  claim 26 , wherein the indole is kynurenic acid, serotonin, nicotinic acid, indole, indole 3-acetic, or indole 3-propionic acid. 
     
     
         28 . The method of any one of  claims 1-27 , wherein the pharmaceutical composition increases levels of indoles in the subject by 2-fold to 100,000-fold. 
     
     
         29 . The method of any one of  claims 1-28 , further comprising administering to the subject an antibiotic. 
     
     
         30 . The method of any one of  claims 1-29 , wherein the subject was administered an antibiotic prior to administration of the pharmaceutical composition. 
     
     
         31 . The method of any one of  claims 1-28 , wherein administration of the pharmaceutical composition is not preceded by administration of an antibiotic. 
     
     
         32 . The method of any one of  claims 29-31 , wherein the antibiotic is vancomycin, fidaxomycin, or ridinilazole. 
     
     
         33 . The method of  claim 32 , wherein the antibiotic is vancomycin. 
     
     
         34 . The method of  claim 33 , wherein the vancomycin is administered at a dose sufficient to allow for colonization of one or more of the bacterial strains of the pharmaceutical composition. 
     
     
         35 . The method of  claim 33 or 34 , wherein the vancomycin is administered in 4 doses of 125 mg per day. 
     
     
         36 . The method of any one of  claims 33-35 , wherein the vancomycin is administered for five consecutive days. 
     
     
         37 . The method of  claim 35 or 36 , wherein the vancomycin is administered on five consecutive days immediately prior to the day of the administration of the pharmaceutical composition. 
     
     
         38 . The method of  claim 35 or 36 , wherein the vancomycin is administered on five consecutive days up to two days prior to the day of the administration of the pharmaceutical composition, and wherein the method includes a washout day one day prior to the day of the administration of the pharmaceutical composition. 
     
     
         39 . The method of any one of  claims 1-38 , wherein the pharmaceutical composition is administered as a single dose. 
     
     
         40 . The method of any one of  claims 1-38 , wherein the pharmaceutical composition is administered in multiple doses. 
     
     
         41 . The method of any one of  claims 1-40 , wherein a dose of the pharmaceutical composition comprises between 10 8  to 10 11  total Colony Forming Units (CFUs). 
     
     
         42 . The method of any one of  claims 1-41 , wherein a dose of the pharmaceutical composition comprises about 10 9  total CFUs. 
     
     
         43 . The method of any one of  claims 1-42 , wherein a dose of the pharmaceutical composition comprises about 10 10  total CFUs. 
     
     
         44 . The method of any one of  claims 39-43 , wherein each dose comprises the administration of multiple capsules. 
     
     
         45 . The method of  claim 44 , wherein each capsule comprises about 10 9  total CFUs. 
     
     
         46 . The method of  claim 44 or 45 , wherein each dose comprises administration of 10 capsules each comprising about 10 9  total CFUs. 
     
     
         47 . The method of any one of  claims 40-46 , wherein the multiple doses are administered on consecutive days. 
     
     
         48 . The method of any one of  claims 40-47 , wherein the multiple doses are administered on 7-14 consecutive days. 
     
     
         49 . The method of any one of  claims 1-48 , wherein the method further comprises administering a therapeutic agent. 
     
     
         50 . The method of  claim 49 , wherein the therapeutic agent is a therapeutic agent for treating IBD or GvHD. 
     
     
         51 . The method of any one of  claims 1-50 , wherein the two or more bacterial strains are lyophilized. 
     
     
         52 . The method of any one of  claims 1-51 , wherein the two or more bacterial strains are spray-dried. 
     
     
         53 . The method of any one of  claims 1-52 , wherein one or more of the two or more bacterial strains are in spore form. 
     
     
         54 . The method of any one of  claims 1-53 , wherein each of the two or more bacterial strains are in spore form. 
     
     
         55 . The method of any one of  claims 1-53 , wherein one or more of the two or more bacterial strains are in vegetative form. 
     
     
         56 . The method of any one of  claim 1-52 or 55 , wherein each of the two or more bacterial strains are in vegetative form. 
     
     
         57 . The method of any one of  claims 1-56 , wherein the pharmaceutical composition further comprises one or more enteric polymers. 
     
     
         58 . The method of any one of  claims 1-57 , wherein the administration is oral administration. 
     
     
         59 . The method of any one of  claims 1-58 , wherein the pharmaceutical composition is formulated for oral delivery. 
     
     
         60 . The method of any one of  claims 1-59 , wherein the pharmaceutical composition is formulated for rectal delivery. 
     
     
         61 . The method of any one of  claims 1-60 , wherein the pharmaceutical composition is formulated for delivery to the intestine. 
     
     
         62 . The method of any one of  claims 1-61 , wherein the pharmaceutical composition is formulated for delivery to the colon. 
     
     
         63 . A method for treating and/or preventing inflammatory bowel disease (IBD) in a subject, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising a purified bacterial mixture comprising two or more bacterial strains of species elected from the group consisting of  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         64 . The method of  claim 63 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen, bacterial strains. 
     
     
         65 . The method of  claim 63 or 64 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         66 . The method of  claim 63 or 64 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium hathewayi, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Eubacterium contortum, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         67 . A method for treating and/or preventing inflammatory bowel disease (IBD) in a subject, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising a purified bacterial mixture comprising two or more bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         68 . The method of  claim 67 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen bacterial strains. 
     
     
         69 . The method of  claim 67 or 68 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         70 . The method of  claim 67 or 68 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 3, 5-10, 12, and 14-16. 
     
     
         71 . The method of any one of  claims 63-70 , wherein the subject is at risk of developing IBD. 
     
     
         72 . The method of  claim 71 , wherein the IBD is ulcerative colitis or Crohn's disease. 
     
     
         73 . The method of any one of  claims 63-72 , wherein the pharmaceutical composition is administered after a first therapeutic agent for treating IBD. 
     
     
         74 . The method of  claim 73 , wherein the first therapeutic for treating IBD is an antibiotic or aminosalicylate (5-ASA) agent. 
     
     
         75 . The method of any one of  claims 63-74 , wherein the subject has one or more risk factors associated with IBD. 
     
     
         76 . The method of any one of  claims 63-75 , wherein each of the bacterial strains of the pharmaceutical composition colonizes the microbiome. 
     
     
         77 . The method of any one of  claims 63-76 , wherein the bacterial strains of the pharmaceutical composition colonize the microbiome over an extended period of time. 
     
     
         78 . The method of any one of  claims 63-77 , wherein the pharmaceutical composition reduces an amount of one or more primary bile acids in the subject. 
     
     
         79 . The method of  claim 78 , wherein the primary bile acid is chenodeoxycholic acid, cholic acid, glycochenodeoxycholic acid, glycocholic acid, taurochenodeoxycholic acid, or taurocholic acid. 
     
     
         80 . The method of any one of  claims 63-79 , wherein the pharmaceutical composition reduces levels of primary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         81 . The method of any one of  claims 63-80 , wherein the pharmaceutical composition increases an amount of one or more secondary bile acids in the subject. 
     
     
         82 . The method of  claim 81 , wherein the secondary bile acid is alloiso isolithocholic acid, dehydrolithocholic acid, deoxycholic acid, glycodeoxycholic acid, glycoursodeoxycholic acid, lithocholic acid, taurodeoxcycholic acid, or ursodeoxycholic acid. 
     
     
         83 . The method of any one of  claims 63-82 , wherein the pharmaceutical composition increases levels of secondary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         84 . The method of any one of  claims 63-83 , wherein the pharmaceutical composition increases an amount of one or more short-chain fatty acids (SCFAs) in the subject. 
     
     
         85 . The method of  claim 84 , wherein the SCFA is 2-methylbutyric acid, acetic acid, butyric acid, hexanoic acid, isobutyric acid, isovaleric acid, propionic acid, or valeric acid. 
     
     
         86 . The method of any one of  claims 63-85 , wherein the pharmaceutical composition increases levels of short-chain fatty acids (SCFAs) in the subject by 2-fold to 100,000-fold. 
     
     
         87 . The method of any one of  claims 63-86 , wherein the pharmaceutical composition increases an amount of one or more indoles in the subject. 
     
     
         88 . The method of  claim 87 , wherein the indole is kynurenic acid, serotonin, nicotinic acid, indole, indole 3-acetic, or indole 3-propionic acid. 
     
     
         89 . The method of any one of  claims 63-88 , wherein the pharmaceutical composition increases levels of indoles in the subject by 2-fold to 100,000-fold. 
     
     
         90 . The method of any one of  claims 63-89 , further comprising administering to the subject an antibiotic. 
     
     
         91 . The method of any one of  claims 63-90 , wherein the subject was administered an antibiotic prior to administration of the pharmaceutical composition. 
     
     
         92 . The method of any one of  claims 63-90 , wherein administration of the pharmaceutical composition is not preceded by administration of an antibiotic. 
     
     
         93 . The method of any one of  claims 90-92 , wherein the antibiotic is vancomycin, fidaxomycin, or ridinilazole. 
     
     
         94 . The method of  claim 93 , wherein the antibiotic is vancomycin. 
     
     
         95 . The method of  claim 94 , wherein the vancomycin is administered at a dose sufficient to allow for colonization of one or more of the bacterial strains of the pharmaceutical composition. 
     
     
         96 . The method of  claim 94 or 95 , wherein the vancomycin is administered in 4 doses of 125 mg per day. 
     
     
         97 . The method of any one of  claims 93-96 , wherein the vancomycin is administered for five consecutive days. 
     
     
         98 . The method of any one of  claims 93-97 , wherein the vancomycin is administered on five consecutive days immediately prior to the day of the administration of the pharmaceutical composition. 
     
     
         99 . The method of any one of  claims 93-97 , wherein the vancomycin is administered on the same day as administration of a first dose of a pharmaceutical composition. 
     
     
         100 . The method of any one of  claims 93-97 , wherein the vancomycin is administered on five consecutive days up to two days prior to the day of the administration of the pharmaceutical composition, and wherein the method includes a washout day one day prior to the day of the administration of the pharmaceutical composition. 
     
     
         101 . The method of any one of  claims 63-100 , wherein the pharmaceutical composition is administered as a single dose. 
     
     
         102 . The method of any one of  claims 63-100 , wherein the pharmaceutical composition is administered in multiple doses. 
     
     
         103 . The method of any one of  claims 63-102 , wherein a dose of the pharmaceutical composition comprises between 10 8  to 10 11  total colony forming units (CFUs). 
     
     
         104 . The method of any one of  claims 63-103 , wherein a dose of the pharmaceutical composition comprises about 10 9  total CFUs. 
     
     
         105 . The method of any one of  claims 63-103 , wherein a dose of the pharmaceutical composition comprises about 10 10  total CFUs. 
     
     
         106 . The method of any one of  claims 101-105 , wherein each dose comprises the administration of multiple capsules. 
     
     
         107 . The method of  claim 106 , wherein each capsule comprises about 10 9  total CFUs. 
     
     
         108 . The method of  claim 106 or 107 , wherein each dose comprises administration of 10 capsules each comprising about 10 9  total CFUs. 
     
     
         109 . The method of any one of  claims 102-108 , wherein the multiple doses are administered on consecutive days. 
     
     
         110 . The method of any one of  claims 102-109 , wherein the multiple doses are administered on 7-14 consecutive days. 
     
     
         111 . The method of any one of  claims 63-110 , wherein the method further comprises administering a therapeutic agent. 
     
     
         112 . The method of  claim 11 , wherein the therapeutic agent is a therapeutic agent for treating IBD. 
     
     
         113 . The method of any one of  claims 63-112 , wherein the two or more bacterial strains are lyophilized. 
     
     
         114 . The method of any one of  claims 63-112 , wherein the two or more bacterial strains are spray-dried. 
     
     
         115 . The method of any one of  claims 63-114 , wherein one or more of the two or more bacterial strains are in spore form. 
     
     
         116 . The method of any one of  claims 63-115 , wherein each of the two or more bacterial strains are in spore form. 
     
     
         117 . The method of any one of  claims 63-115 , wherein one or more of the two or more bacterial strains are in vegetative form. 
     
     
         118 . The method of any one of  claims 63-114 and 117 , wherein each of the two or more bacterial strains are in vegetative form. 
     
     
         119 . The method of any one of  claims 63-118 , wherein the pharmaceutical composition further comprises one or more enteric polymers. 
     
     
         120 . The method of any one of  claims 63-119 , wherein the administration is oral administration. 
     
     
         121 . The method of any one of  claims 63-120 , wherein the pharmaceutical composition is formulated for oral delivery. 
     
     
         122 . The method of any one of  claims 63-120 , wherein the pharmaceutical composition is formulated for rectal delivery. 
     
     
         123 . The method of any one of  claims 63-122 , wherein the pharmaceutical composition is formulated for delivery to the intestine. 
     
     
         124 . The method of any one of  claims 63-123 , wherein the pharmaceutical composition is formulated for delivery to the colon. 
     
     
         125 . A method for reducing risk and/or occurrence of inflammatory bowel disease (IBD) in a subject, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising a purified bacterial mixture comprising two or more bacterial strains of species elected from the group consisting of  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         126 . The method of  claim 125 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen, bacterial strains. 
     
     
         127 . The method of  claim 125 or 126 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         128 . The method of  claim 125 or 126 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium hathewayi, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Eubacterium contortum, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         129 . A method for reducing risk and/or occurrence of inflammatory bowel disease (IBD) in a subject, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising a purified bacterial mixture comprising two or more bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         130 . The method of  claim 129 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen bacterial strains. 
     
     
         131 . The method of  claim 129 or 130 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         132 . The method of  claim 129 or 130 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 3, 5-10, 12, and 14-16. 
     
     
         133 . The method of any one of  claims 125-132 , wherein the IBD is ulcerative colitis or Crohn's disease. 
     
     
         134 . The method of any one of  claims 125-133 , wherein the pharmaceutical composition is administered after a first therapeutic agent for treating IBD. 
     
     
         135 . The method of  claim 134 , wherein the first therapeutic for treating IBD is an antibiotic or aminosalicylate (5-ASA) agent. 
     
     
         136 . The method of any one of  claims 125-135 , wherein the subject has one or more risk factors associated with IBD. 
     
     
         137 . The method of any one of  claims 125-136 , wherein each of the bacterial strains of the pharmaceutical composition colonizes the microbiome. 
     
     
         138 . The method of any one of  claims 125-137 , wherein the bacterial strains of the pharmaceutical composition colonize the microbiome over an extended period of time. 
     
     
         139 . The method of any one of  claims 125-138 , wherein the pharmaceutical composition reduces an amount of one or more primary bile acids in the subject. 
     
     
         140 . The method of  claim 139 , wherein the primary bile acid is chenodeoxycholic acid, cholic acid, glycochenodeoxycholic acid, glycocholic acid, taurochenodeoxycholic acid, or taurocholic acid. 
     
     
         141 . The method of any one of  claims 125-140 , wherein the pharmaceutical composition reduces levels of primary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         142 . The method of any one of  claims 125-141 , wherein the pharmaceutical composition increases an amount of one or more secondary bile acids in the subject. 
     
     
         143 . The method of  claim 142 , wherein the secondary bile acid is alloiso isolithocholic acid, dehydrolithocholic acid, deoxycholic acid, glycodeoxycholic acid, glycoursodeoxycholic acid, lithocholic acid, taurodeoxcycholic acid, or ursodeoxycholic acid. 
     
     
         144 . The method of any one of  claims 125-143 , wherein the pharmaceutical composition increases levels of secondary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         145 . The method of any one of  claims 125-144 , wherein the pharmaceutical composition increases an amount of one or more short-chain fatty acids (SCFAs) in the subject. 
     
     
         146 . The method of  claim 145 , wherein the SCFA is 2-methylbutyric acid, acetic acid, butyric acid, hexanoic acid, isobutyric acid, isovaleric acid, propionic acid, or valeric acid. 
     
     
         147 . The method of any one of  claims 125-146 , wherein the pharmaceutical composition increases levels of short-chain fatty acids (SCFAs) in the subject by 2-fold to 100,000-fold. 
     
     
         148 . The method of any one of  claims 125-147 , wherein the pharmaceutical composition increases an amount of one or more indoles in the subject. 
     
     
         149 . The method of  claim 148 , wherein the indole is kynurenic acid, serotonin, nicotinic acid, indole, indole 3-acetic, or indole 3-propionic acid. 
     
     
         150 . The method of any one of  claims 125-149 , wherein the pharmaceutical composition increases levels of indoles in the subject by 2-fold to 100,000-fold. 
     
     
         151 . The method of any one of  claims 125-150 , further comprising administering to the subject an antibiotic. 
     
     
         152 . The method of any one of  claims 125-151 , wherein the subject was administered an antibiotic prior to administration of the pharmaceutical composition. 
     
     
         153 . The method of any one of  claims 125-151 , wherein administration of the pharmaceutical composition is not preceded by administration of an antibiotic. 
     
     
         154 . The method of any one of  claims 151-153 , wherein the antibiotic is vancomycin, fidaxomycin, or ridinilazole. 
     
     
         155 . The method of  claim 154 , wherein the antibiotic is vancomycin. 
     
     
         156 . The method of  claim 155 , wherein the vancomycin is administered at a dose sufficient to allow for colonization of one or more of the bacterial strains of the pharmaceutical composition. 
     
     
         157 . The method of  claim 155 or 156 , wherein the vancomycin is administered in 4 doses of 125 mg per day. 
     
     
         158 . The method of any one of  claims 155-157 , wherein the vancomycin is administered for five consecutive days. 
     
     
         159 . The method of any one of  claims 153-158 , wherein the vancomycin is administered on five consecutive days immediately prior to the day of the administration of the pharmaceutical composition. 
     
     
         160 . The method of any one of  claims 153-158 , wherein the vancomycin is administered on the same day as administration of a first dose of a pharmaceutical composition. 
     
     
         161 . The method of any one of  claims 153-158 , wherein the vancomycin is administered on five consecutive days up to two days prior to the day of the administration of the pharmaceutical composition, and wherein the method includes a washout day one day prior to the day of the administration of the pharmaceutical composition. 
     
     
         162 . The method of any one of  claims 125-161 , wherein the pharmaceutical composition is administered as a single dose. 
     
     
         163 . The method of any one of  claims 125-161 , wherein the pharmaceutical composition is administered in multiple doses. 
     
     
         164 . The method of any one of  claims 125-161 , wherein a dose of the pharmaceutical composition comprises between 10 8  to 10 11  total colony forming units (CFUs). 
     
     
         165 . The method of any one of  claims 162-164 , wherein a dose of the pharmaceutical composition comprises about 10 9  total CFUs. 
     
     
         166 . The method of any one of  claims 162-164 , wherein a dose of the pharmaceutical composition comprises about 10 10  total CFUs. 
     
     
         167 . The method of any one of  claims 162-166 , wherein each dose comprises the administration of multiple capsules. 
     
     
         168 . The method of  claim 167 , wherein each capsule comprises about 10 9  total CFUs. 
     
     
         169 . The method of  claim 167 or 168 , wherein each dose comprises administration of 10 capsules each comprising about 10 9  total CFUs. 
     
     
         170 . The method of any one of  claims 163-169 , wherein the multiple doses are administered on consecutive days. 
     
     
         171 . The method of any one of  claims 163-170 , wherein the multiple doses are administered on 7-14 consecutive days. 
     
     
         172 . The method of any one of  claims 125-171 , wherein the method further comprises administering a therapeutic agent. 
     
     
         173 . The method of  claim 171 , wherein the therapeutic agent is a therapeutic agent for treating IBD. 
     
     
         174 . The method of any one of  claims 125-173 , wherein the two or more bacterial strains are lyophilized. 
     
     
         175 . The method of any one of  claims 125-173 , wherein the two or more bacterial strains are spray-dried. 
     
     
         176 . The method of any one of  claims 125-175 , wherein one or more of the two or more bacterial strains are in spore form. 
     
     
         177 . The method of any one of  claims 125-176 , wherein each of the two or more bacterial strains are in spore form. 
     
     
         178 . The method of any one of  claims 125-176 , wherein one or more of the two or more bacterial strains are in vegetative form. 
     
     
         179 . The method of any one of  claims 125-177 and 178 , wherein each of the two or more bacterial strains are in vegetative form. 
     
     
         180 . The method of any one of  claims 125-179 , wherein the pharmaceutical composition further comprises one or more enteric polymers. 
     
     
         181 . The method of any one of  claims 125-180 , wherein the administration is oral administration. 
     
     
         182 . The method of any one of  claims 125-181 , wherein the pharmaceutical composition is formulated for oral delivery. 
     
     
         183 . The method of any one of  claims 125-182 , wherein the pharmaceutical composition is formulated for rectal delivery. 
     
     
         184 . The method of any one of  claims 125-183 , wherein the pharmaceutical composition is formulated for delivery to the intestine. 
     
     
         185 . The method of any one of  claims 125-184 , wherein the pharmaceutical composition is formulated for delivery to the colon. 
     
     
         186 . A method for treating and/or preventing graft versus host disease (GvHD) in a subject, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising a purified bacterial mixture comprising two or more bacterial strains of species selected from the group consisting of  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         187 . The method of  claim 186 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen, bacterial strains. 
     
     
         188 . The method of  claim 186 or 187 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         189 . The method of  claim 186 or 187 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium hathewayi, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Eubacterium contortum, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         190 . A method for treating and/or preventing graft versus host disease (GvHD) in a subject, the method comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising a purified bacterial mixture comprising two or more bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         191 . The method of  claim 190 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen bacterial strains. 
     
     
         192 . The method of  claim 190 or 191 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         193 . The method of  claim 190 or 191 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 3, 5-10, 12, and 14-16. 
     
     
         194 . The method of any one of  claims 186-193 , wherein the subject is at risk of developing GvHD. 
     
     
         195 . The method of any one of  claims 186-194 , wherein the pharmaceutical composition is administered after a first therapeutic agent for treating GvHD. 
     
     
         196 . The method of any one of  claims 186-195 , wherein each of the bacterial strains of the pharmaceutical composition colonizes the microbiome. 
     
     
         197 . The method of any one of  claims 186-196 , wherein the bacterial strains of the pharmaceutical composition colonize the microbiome over an extended period of time. 
     
     
         198 . The method of any one of  claims 186-197 , wherein the pharmaceutical composition reduces an amount of one or more primary bile acids in the subject. 
     
     
         199 . The method of  claim 198 , wherein the primary bile acid is chenodeoxycholic acid, cholic acid, glycochenodeoxycholic acid, glycocholic acid, taurochenodeoxycholic acid, or taurocholic acid. 
     
     
         200 . The method of any one of  claims 186-199 , wherein the pharmaceutical composition reduces levels of primary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         201 . The method of any one of  claims 186-200 , wherein the pharmaceutical composition increases an amount of one or more secondary bile acids in the subject. 
     
     
         202 . The method of  claim 201 , wherein the secondary bile acid is alloiso isolithocholic acid, dehydrolithocholic acid, deoxycholic acid, glycodeoxycholic acid, glycoursodeoxycholic acid, lithocholic acid, taurodeoxcycholic acid, or ursodeoxycholic acid. 
     
     
         203 . The method of any one of  claims 186-202 , wherein the pharmaceutical composition increases levels of secondary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         204 . The method of any one of  claims 186-203 , wherein the pharmaceutical composition increases an amount of one or more short-chain fatty acids (SCFAs) in the subject. 
     
     
         205 . The method of  claim 204 , wherein the SCFA is 2-methylbutyric acid, acetic acid, butyric acid, hexanoic acid, isobutyric acid, isovaleric acid, propionic acid, or valeric acid. 
     
     
         206 . The method of any one of  claims 186-205 , wherein the pharmaceutical composition increases levels of short-chain fatty acids (SCFAs) in the subject by 2-fold to 100,000-fold. 
     
     
         207 . The method of any one of  claims 186-206 , wherein the pharmaceutical composition increases an amount of one or more indoles in the subject. 
     
     
         208 . The method of  claim 207 , wherein the indole is kynurenic acid, serotonin, nicotinic acid, indole, indole 3-acetic, or indole 3-propionic acid. 
     
     
         209 . The method of any one of  claims 186-208 , wherein the pharmaceutical composition increases levels of indoles in the subject by 2-fold to 100,000-fold. 
     
     
         210 . The method of any one of  claims 186-209 , further comprising administering to the subject an antibiotic. 
     
     
         211 . The method of any one of  claims 186-210 , wherein the subject was administered an antibiotic prior to administration of the pharmaceutical composition. 
     
     
         212 . The method of any one of  claims 186-210 , wherein administration of the pharmaceutical composition is not preceded by administration of an antibiotic. 
     
     
         213 . The method of any one of  claims 210-212 , wherein the antibiotic is vancomycin, fidaxomycin, or ridinilazole. 
     
     
         214 . The method of  claim 213 , wherein the antibiotic is vancomycin. 
     
     
         215 . The method of  claim 214 , wherein the vancomycin is administered at a dose sufficient to allow for colonization of one or more of the bacterial strains of the pharmaceutical composition. 
     
     
         216 . The method of  claim 214 or 215 , wherein the vancomycin is administered in 4 doses of 125 mg per day. 
     
     
         217 . The method of any one of  claims 214-216 , wherein the vancomycin is administered for five consecutive days. 
     
     
         218 . The method of any one of  claims 214-217 , wherein the vancomycin is administered on five consecutive days immediately prior to the day of the administration of the pharmaceutical composition. 
     
     
         219 . The method of any one of  claims 214-218 , wherein the vancomycin is administered on the same day as administration of a first dose of a pharmaceutical composition. 
     
     
         220 . The method of any one of  claims 214-218 , wherein the vancomycin is administered on five consecutive days up to two days prior to the day of the administration of the pharmaceutical composition, and wherein the method includes a washout day one day prior to the day of the administration of the pharmaceutical composition. 
     
     
         221 . The method of any one of  claims 186-220 , wherein the pharmaceutical composition is administered as a single dose. 
     
     
         222 . The method of any one of  claims 186-220 , wherein the pharmaceutical composition is administered in multiple doses. 
     
     
         223 . The method of any one of claims  186 - 2223 , wherein a dose of the pharmaceutical composition comprises between 10 8  to 10 11  total colony forming units (CFUs). 
     
     
         224 . The method of any one of  claims 186-223 , wherein a dose of the pharmaceutical composition comprises about 10 9  total CFUs. 
     
     
         225 . The method of any one of  claims 186-224 , wherein a dose of the pharmaceutical composition comprises about 10 10  total CFUs. 
     
     
         226 . The method of any one of  claims 221-225 , wherein each dose comprises the administration of multiple capsules. 
     
     
         227 . The method of  claim 226 , wherein each capsule comprises about 10 9  total CFUs. 
     
     
         228 . The method of  claim 226 or 227 , wherein each dose comprises administration of 10 capsules each comprising about 10 9  total CFUs. 
     
     
         229 . The method of any one of  claims 222-228 , wherein the multiple doses are administered on consecutive days. 
     
     
         230 . The method of any one of  claims 222-229 , wherein the multiple doses are administered on 7-14 consecutive days. 
     
     
         231 . The method of any one of  claims 186-230 , wherein the method further comprises administering a therapeutic agent. 
     
     
         232 . The method of  claim 231 , wherein the therapeutic agent is a therapeutic agent for treating GvHD. 
     
     
         233 . The method of any one of  claims 186-232 , wherein the two or more bacterial strains are lyophilized. 
     
     
         234 . The method of any one of  claims 186-232 , wherein the two or more bacterial strains are spray-dried. 
     
     
         235 . The method of any one of  claims 186-234 , wherein one or more of the two or more bacterial strains are in spore form. 
     
     
         236 . The method of any one of  claims 186-235 , wherein each of the two or more bacterial strains are in spore form. 
     
     
         237 . The method of any one of  claims 186-235 , wherein one or more of the two or more bacterial strains are in vegetative form. 
     
     
         238 . The method of any one of  claims 186-234 and 237 , wherein each of the two or more bacterial strains are in vegetative form. 
     
     
         239 . The method of any one of  claims 186-238 , wherein the pharmaceutical composition further comprises one or more enteric polymers. 
     
     
         240 . The method of any one of  claims 186-239 , wherein the administration is oral administration. 
     
     
         241 . The method of any one of  claims 186-240 , wherein the pharmaceutical composition is formulated for oral delivery. 
     
     
         242 . The method of any one of  claims 186-240 , wherein the pharmaceutical composition is formulated for rectal delivery. 
     
     
         243 . The method of any one of  claims 186-242 , wherein the pharmaceutical composition is formulated for delivery to the intestine. 
     
     
         244 . The method of any one of  claims 186-243 , wherein the pharmaceutical composition is formulated for delivery to the colon. 
     
     
         245 . A method, comprising administering to a subject a therapeutically effective amount of a pharmaceutical composition in a loading period followed by administering to the subject a therapeutically effective amount of the pharmaceutical composition a maintenance period, wherein the pharmaceutical composition comprises a purified bacterial mixture comprising two or more bacterial strains of species selected from the group consisting of  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         246 . The method of  claim 245 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen, bacterial strains. 
     
     
         247 . The method of  claim 245 or 246 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium saccharogumia, Flavonifractor plautii, Clostridium hathewayi, Blautia coccoides, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Clostridium ramosum, Eubacterium contortum, Clostridium scindens, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         248 . The method of  claim 245 or 246 , wherein the purified bacterial mixture consists of bacterial strains of species  Clostridium hathewayi, Clostridium bolteae, Clostridium indolis, Anaerotruncus colihominis, Ruminococcus  sp.,  Clostridium lavalense, Clostridium symbiosum, Eubacterium contortum, Lachnospiraceae bacterium, Clostridium  sp., and  Lachnospiraceae bacterium.    
     
     
         249 . A method, comprising administering to a subject a therapeutically effective amount of a pharmaceutical composition in a loading period followed by administering to the subject a therapeutically effective amount of the pharmaceutical composition a maintenance period, wherein the pharmaceutical composition comprises a purified bacterial mixture comprising two or more bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         250 . The method of  claim 249 , wherein the purified bacterial mixture comprises at least three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen bacterial strains. 
     
     
         251 . The method of  claim 249 or 250 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 1-16. 
     
     
         252 . The method of  claim 249 or 250 , wherein the pharmaceutical composition comprises a purified bacterial mixture consisting of bacterial strains that comprise 16S rDNA sequences of at least 97% sequence identity to the nucleic acid sequences set forth as SEQ ID NOs: 3, 5-10, 12, and 14-16. 
     
     
         253 . The method of any one of  claims 245-252 , wherein the pharmaceutical composition reduces an amount of one or more primary bile acids in the subject. 
     
     
         254 . The method of  claim 253 , wherein the primary bile acid is chenodeoxycholic acid, cholic acid, glycochenodeoxycholic acid, glycocholic acid, taurochenodeoxycholic acid, or taurocholic acid. 
     
     
         255 . The method of any one of  claims 245-254 , wherein the pharmaceutical composition reduces levels of primary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         256 . The method of any one of  claims 245-255 , wherein the pharmaceutical composition increases an amount of one or more secondary bile acids in the subject. 
     
     
         257 . The method of  claim 256 , wherein the secondary bile acid is alloiso isolithocholic acid, dehydrolithocholic acid, deoxycholic acid, glycodeoxycholic acid, glycoursodeoxycholic acid, lithocholic acid, taurodeoxcycholic acid, or ursodeoxycholic acid. 
     
     
         258 . The method of any one of  claims 245-257 , wherein the pharmaceutical composition increases levels of secondary bile acids in the subject by 2-fold to 100,000-fold. 
     
     
         259 . The method of any one of  claims 245-258 , wherein the pharmaceutical composition increases an amount of one or more short-chain fatty acids (SCFAs) in the subject. 
     
     
         260 . The method of  claim 259 , wherein the SCFA is 2-methylbutyric acid, acetic acid, butyric acid, hexanoic acid, isobutyric acid, isovaleric acid, propionic acid, or valeric acid. 
     
     
         261 . The method of any one of  claims 249-260 , wherein the pharmaceutical composition increases levels of short-chain fatty acids (SCFAs) in the subject by 2-fold to 100,000-fold. 
     
     
         262 . The method of any one of  claims 245-261 , wherein the pharmaceutical composition increases an amount of one or more indoles in the subject. 
     
     
         263 . The method of  claim 262 , wherein the indole is kynurenic acid, serotonin, nicotinic acid, indole, indole 3-acetic, or indole 3-propionic acid. 
     
     
         264 . The method of any one of  claims 245-263 , wherein the pharmaceutical composition increases levels of indoles in the subject by 2-fold to 100,000-fold. 
     
     
         265 . The method of any one of  claims 245-264 , further comprising administering to the subject an antibiotic prior to the loading period. 
     
     
         266 . The method of  claim 265 , wherein the loading period is not preceded by administration of an antibiotic. 
     
     
         267 . The method of  claim 265 or 266 , wherein the antibiotic is vancomycin, fidaxomycin, or ridinilazole. 
     
     
         268 . The method of  claim 267 , wherein the antibiotic is vancomycin. 
     
     
         269 . The method of any one of  claims 245-268 , wherein the loading period is at least 7 days and a loading dose of the pharmaceutical composition is administered to the subject at least every 3 days for the loading period. 
     
     
         270 . The method of  claim 269 , wherein the loading period is between 7 and 14 days. 
     
     
         271 . The method of  claim 269 or 270 , wherein the loading dose of the pharmaceutical composition is administered to the subject daily for the loading period. 
     
     
         272 . The method of any one of  claims 245-271 , wherein the maintenance period is 6 weeks, and a maintenance dose of the pharmaceutical composition is administered to the subject daily for the maintenance period. 
     
     
         273 . The method of any one of  claim 272 , wherein the maintenance dose comprises fewer total colony forming units as compared to the loading dose. 
     
     
         274 . The method of any one of  claims 245-273 , wherein the loading period and maintenance period are repeated every 2 months, 3 months, 4 months, 5 months, 6 months, 12 months, 18 months, or 24 months. 
     
     
         275 . The method of any one of  claims 245-274 , wherein the two or more bacterial strains are lyophilized. 
     
     
         276 . The method of any one of  claims 245-275 , wherein the two or more bacterial strains are spray-dried. 
     
     
         277 . The method of any one of  claims 245-276 , wherein one or more of the two or more bacterial strains are in spore form. 
     
     
         278 . The method of any one of  claims 245-277 , wherein each of the two or more bacterial strains are in spore form. 
     
     
         279 . The method of any one of  claims 245-277 , wherein one or more of the two or more bacterial strains are in vegetative form. 
     
     
         280 . The method of any one of  claims 245-276 and 279 , wherein each of the two or more bacterial strains are in vegetative form. 
     
     
         281 . The method of any one of  claims 245-280 , wherein the pharmaceutical composition further comprises one or more enteric polymers. 
     
     
         282 . The method of any one of  claims 245-281 , wherein the administration is oral administration. 
     
     
         283 . The method of any one of  claims 245-282 , wherein the pharmaceutical composition is formulated for oral delivery. 
     
     
         284 . The method of any one of  claims 245-282 , wherein the pharmaceutical composition is formulated for rectal delivery. 
     
     
         285 . The method of any one of  claims 245-284 , wherein the pharmaceutical composition is formulated for delivery to the intestine. 
     
     
         286 . The method of any one of  claims 245-285 , wherein the pharmaceutical composition is formulated for delivery to the colon. 
     
     
         287 . A method for assessing colonization of one or more bacterial strains of a bacterial composition in a microbiome of a subject, the method comprising
 isolating nucleic acid from a sample of the microbiome of the subject; and   determining the presence of at least one bacterial strain of the bacterial composition by amplifying a nucleotide sequence of a genomic marker for the at least one the bacterial strains in the isolated nucleic acid;   wherein if a genomic marker for a bacterial strain is present in the amplified nucleotide sequences, the microbiome is colonized with the bacterial strain.   
     
     
         288 . The method of  claim 287 , wherein amplifying comprises performing one or more quantitative polymerase chain reactions (qPCR). 
     
     
         289 . The method of  claim 287 or 288 , wherein the qPCR is performed using one or more pair of primers, wherein each pair of primers comprises a forward primer and a reverse primer for amplifying the nucleotide sequence of the genomic marker of bacterial strain. 
     
     
         290 . The method of  claim 289 , wherein the pair of primers for amplifying the nucleotide sequence of the genomic marker of comprises the forward primer set forth in any one of SEQ ID NOs: 17-32 and the reverse primer set forth in any one of SEQ ID NOs: 33-48. 
     
     
         291 . The method of any one of  claims 288-290 , wherein the qPCR reaction further comprises a DNA probe. 
     
     
         292 . The method of  claim 291 , wherein the DNA probe comprises a fluorophore and at least one quencher. 
     
     
         293 . The method of  claim 291 or 292 , wherein the DNA probe comprises a sequence that is present in any one of the sequences set forth in SEQ ID NOs: 49-64. 
     
     
         294 . The method of any one of  claims 287-293 , wherein if a genomic marker for a bacterial strain is absent in the amplified nucleotide sequences, the method further comprises administering one or more additional doses of the bacterial composition to the subject.